To evaluate if habenular nuclei lesions improve, impair, or have no effects on two-way active avoidance acquisition and/or retention, rats in a lesion group were subjected to bilateral electrolytical lesions of this complex, while control rats were sham-operated (Sham group). Once recovered from the stereotaxic procedures, rats were submitted to 5 training sessions (10 trials each, one session per day) of two-way active avoidance conditioning. Ten days after the last training session, another session was administered in order to test the long-term retention of the task. Results indicated that habenular lesions did not affect the overall performance of the rats during either the acquisition sessions or the retention session of two-way active avoidance. We suggest that habenular lesions can affect the acquisition of several learning tasks, probably through their role in modulating stress responses and/or arousal states. The nature of these effects (whether facilitatative, detrimental, or neutral) might depend on the interaction between several factors such as the kind of task, the specific conditioning procedures (which may generate different stress levels), and the specific area destroyed by the lesion.